Metabolic Changes in Scylla paramamosain During Adaptation to an Acute Decrease in Salinity

The mud crab Scylla paramamosain is an important euryhaline mariculture species. However, acute decreases in salinity seriously impact its survival and can result in large production losses. In this study, we evaluated metabolic changes in S. paramamosain exposed to an acute salinity reduction from 23 psu to 3 psu. After the salinity decrease, hemolymph osmolality declined from 726.75 to 642.38 mOsm/kg H2O, which was close to the physiological equilibrium state. Activities of osmolality regulation-related enzymes in the gills, including Na+-K+-ATPase, CA, and V-ATPase all increased. Using LC-MS analysis, we identified 519 metabolites (mainly lipids). Additionally, 13 significant metabolic pathways (P < 0.05) were identified via enrichment analysis, which were mainly related to signal pathways, lipids, and transportation. Our correlation analysis, which combined LC-MS and previous GC-MS data, yielded 28 significant metabolic pathways. Amino acids and energy metabolism accounted for most of these pathways, and lipid metabolism pathways were insignificant. Our results showed that amino acids and energy metabolism were the dominant factors involved in the adaptation of S. paramamosain to acute salinity decrease, and lipid metabolites played a supporting role.

Download Full-text

Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review

Food Science and Biotechnology ◽

10.1007/s10068-021-00917-9 ◽

2021 ◽

Author(s):

Min Kyung Park ◽

Young-Suk Kim

Keyword(s):

Mass Spectrometry ◽

Amino Acids ◽

Metabolic Pathways ◽

Metabolic Changes ◽

Fermented Foods ◽

Organoleptic Properties ◽

Efficient Tool ◽

Microbial Enzymes ◽

Volatile Metabolites ◽

Quantitative Analyses

AbstractMetabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.

Download Full-text

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

Microorganisms ◽

10.3390/microorganisms9081789 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1789

Author(s):

Suprokash Koner ◽

Jung-Sheng Chen ◽

Bing-Mu Hsu ◽

Chao-Wen Tan ◽

Cheng-Wei Fan ◽

...

Keyword(s):

Amino Acids ◽

Microbial Community ◽

Energy Metabolism ◽

Carbon Source ◽

16S Rrna ◽

Bacterial Communities ◽

Metabolic Pathways ◽

Carbon Substrate ◽

Carbon Utilization ◽

Biolog Ecoplate

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Download Full-text

Synthesis and Breakdown of the Universal Precursors to Biological Metabolism Promoted by Ferrous Iron

10.26434/chemrxiv.7178930.v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Kamila B. Muchowska ◽

Sreejith Jayasree VARMA ◽

Joseph Moran

Keyword(s):

Amino Acids ◽

Chemical Reaction ◽

Metabolic Pathways ◽

Ferrous Iron ◽

Reaction Network ◽

Tca Cycle ◽

Chemical Reaction Network ◽

Metabolic Precursors ◽

Tca Cycle Intermediates

How core biological metabolism initiated and why it uses the intermediates, reactions and pathways that it does remains unclear. Life builds its molecules from CO2 and breaks them down to CO2 again through the intermediacy of just five metabolites that act as the hubs of biochemistry. Here, we describe a purely chemical reaction network promoted by Fe2+ in which aqueous pyruvate and glyoxylate, two products of abiotic CO2 reduction, build up nine of the eleven TCA cycle intermediates, including all five universal metabolic precursors. The intermediates simultaneously break down to CO2 in a life-like regime resembling biological anabolism and catabolism. Introduction of hydroxylamine and Fe0 produces four biological amino acids. The network significantly overlaps the TCA/rTCA and glyoxylate cycles and may represent a prebiotic precursor to these core metabolic pathways.

Download Full-text

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

Bulletin of Entomological Research ◽

10.1017/s0007485321000171 ◽

2021 ◽

pp. 1-14

Author(s):

Peirong Li ◽

Xinru Li ◽

Wei Wang ◽

Xiaoling Tan ◽

Xiaoqi Wang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Developmental Stages ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Mythimna Separata ◽

Kegg Pathway Analysis ◽

Oriental Armyworm ◽

Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

Download Full-text

Physiological and Proteomic Responses of Pitaya to PEG-Induced Drought Stress

Agriculture ◽

10.3390/agriculture11070632 ◽

2021 ◽

Vol 11 (7) ◽

pp. 632

Author(s):

Aihua Wang ◽

Chao Ma ◽

Hongye Ma ◽

Zhilang Qiu ◽

Xiaopeng Wen

Keyword(s):

Drought Stress ◽

Energy Metabolism ◽

Metabolic Pathways ◽

Treatment Time ◽

Soluble Sugar ◽

Antioxidant Systems ◽

Antioxidant Enzyme Activities ◽

Proteomic Data ◽

Proteome Profile ◽

Proteomic Responses

Pitaya (Hylocereus polyrhizus L.) is highly tolerant to drought stress. Elucidating the response mechanism of pitaya to drought will substantially contribute to improving crop drought tolerance. In the present study, the physiological and proteomic responses of the pitaya cultivar ‘Zihonglong’ were compared between control seedlings and seedlings exposed to drought stress (−4.9 MPa) induced by polyethylene glycol for 7 days. Drought stress obviously enhanced osmolyte accumulation, lipid peroxidation, and antioxidant enzyme activities. Proteomic data revealed drought stress activated several pathways in pitaya, including carbohydrate and energy metabolism at two drought stress treatment time-points (6 h and 3 days). Other metabolic pathways, including those related to aspartate, glutamate, glutathione, and secondary metabolites, were induced more at 3 days than at 6 h, whereas photosynthesis and arginine metabolism were induced exclusively at 6 h. Overall, protein expression changes were consistent with the physiological responses, although there were some differences in the timing. The increases in soluble sugar contents mainly resulted from the degradation and transformation of insoluble carbohydrates. Differentially accumulated proteins in amino acid metabolism may be important for the conversion and accumulation of amino acids. GSH and AsA metabolism and secondary metabolism may play important roles in pitaya as enzymatic and nonenzymatic antioxidant systems. The enhanced carbohydrate and energy metabolism may provide the energy necessary for initiating the above metabolic pathways. The current study provided the first proteome profile of this species exposed to drought stress, and may clarify the mechanisms underlying the considerable tolerance of pitaya to drought stress.

Download Full-text

Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

Scientific Reports ◽

10.1038/s41598-021-92317-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Huanyong Li ◽

Xiaoqian Tang ◽

Xiuyan Yang ◽

Huaxin Zhang

Keyword(s):

Salt Stress ◽

Amino Acid ◽

Salt Tolerance ◽

Metabolic Pathways ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Sulfur Metabolism ◽

Enrichment Analysis ◽

Extracellular Region ◽

Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

Download Full-text

Radical Hemithoracic Radiotherapy Induces Systemic Metabolomics Changes That Are Associated with the Clinical Outcome of Malignant Pleural Mesothelioma Patients

Cancers ◽

10.3390/cancers13030508 ◽

2021 ◽

Vol 13 (3) ◽

pp. 508

Author(s):

Emanuela Di Gregorio ◽

Gianmaria Miolo ◽

Asia Saorin ◽

Elena Muraro ◽

Michela Cangemi ◽

...

Keyword(s):

Amino Acids ◽

Overall Survival ◽

Clinical Outcome ◽

Malignant Pleural Mesothelioma ◽

Therapeutic Option ◽

Enrichment Analysis ◽

Metabolic Effects ◽

Pleural Mesothelioma ◽

Polyamine Biosynthesis ◽

The Individual

Radical hemithoracic radiotherapy (RHRT) represents an advanced therapeutic option able to improve overall survival of malignant pleural mesothelioma patients. This study aims to investigate the systemic effects of this radiotherapy modality on the serum metabolome and their potential implications in determining the individual clinical outcome. Nineteen patients undergoing RHRT at the dose of 50 Gy in 25 fractions were enrolled. Serum targeted metabolomics profiles were investigated at baseline and the end of radiotherapy by liquid chromatography and tandem mass spectrometry. Univariate and multivariate OPLS-DA analyses were applied to study the serum metabolomics changes induced by RHRT while PLS regression analysis to evaluate the association between such changes and overall survival. RHRT was found to affect almost all investigated metabolites classes, in particular, the amino acids citrulline and taurine, the C14, C18:1 and C18:2 acyl-carnitines as well as the unsaturated long chain phosphatidylcholines PC ae 42:5, PC ae 44:5 and PC ae 44:6 were significantly decreased. The enrichment analysis showed arginine metabolism and the polyamine biosynthesis as the most perturbed pathways. Moreover, specific metabolic changes encompassing the amino acids and acyl-carnitines resulted in association with the clinical outcome accounting for about 60% of the interpatients overall survival variability. This study highlighted that RHRT can induce profound systemic metabolic effects some of which may have a significant prognostic value. The integration of metabolomics in the clinical assessment of the malignant pleural mesothelioma could be useful to better identify the patients who can achieve the best benefit from the RHRT treatment.

Download Full-text

Metabolomic profiling of anaerobic and aerobic energy metabolic pathways in chronic obstructive pulmonary disease

Experimental Biology and Medicine ◽

10.1177/15353702211008808 ◽

2021 ◽

pp. 153537022110088

Author(s):

Mingshan Xue ◽

Yifeng Zeng ◽

Runpei Lin ◽

Hui-Qi Qu ◽

Teng Zhang ◽

...

Keyword(s):

Chronic Obstructive Pulmonary Disease ◽

Energy Metabolism ◽

Pulmonary Disease ◽

Metabolic Pathways ◽

Energy Supply ◽

Stable Phase ◽

Chronic Obstructive ◽

Obstructive Pulmonary Disease ◽

Copd Patients ◽

Anaerobic Energy

While there is no cure for chronic obstructive pulmonary disease (COPD), its progressive nature and the formidable challenge to manage its symptoms warrant a more extensive study of the pathogenesis and related mechanisms. A new emphasis on COPD study is the change of energy metabolism. For the first time, this study investigated the anaerobic and aerobic energy metabolic pathways in COPD using the metabolomic approach. Metabolomic analysis was used to investigate energy metabolites in 140 COPD patients. The significance of energy metabolism in COPD was comprehensively explored by the Global Initiative for Chronic Obstructive Lung Disease–GOLD grading, acute exacerbation vs. stable phase (either clinical stability or four-week stable phase), age group, smoking index, lung function, and COPD Assessment Test (CAT) score. Through comprehensive evaluation, we found that COPD patients have a significant imbalance in the aerobic and anaerobic energy metabolisms in resting state, and a high tendency of anaerobic energy supply mechanism that correlates positively with disease progression. This study highlighted the significance of anaerobic and low-efficiency energy supply pathways in lung injury and linked it to the energy-inflammation-lung ventilatory function and the motion limitation mechanism in COPD patients, which implies a novel therapeutic direction for this devastating disease.

Download Full-text

Identification of novel cardiovascular disease associated metabolites using untargeted metabolomics

Biological Chemistry ◽

10.1515/hsz-2020-0331 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Shams Tabrez ◽

Mohammed Razeeth Shait Mohammed ◽

Nasimudeen R. Jabir ◽

Mohammad Imran Khan

Keyword(s):

Cardiovascular Disease ◽

Metabolic Pathways ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Healthy Individuals ◽

Great Opportunity ◽

Pathway Enrichment ◽

Pathophysiological Role ◽

The World ◽

Metabolomic Approach

Abstract Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality around the world. Early diagnosis of CVD could provide the opportunity for sensible management and better clinical outcome along with the prevention of further progression of the disease. In the current study, we used an untargeted metabolomic approach to identify possible metabolite(s) that associate well with the CVD and could serve either as therapeutic target or disease-associated metabolite. We identified 26 rationally adjusted unique metabolites that were differentially present in the serum of CVD patients compared with healthy individuals, among them 15 were found to be statistically significant. Out of these metabolites, we identified some novel metabolites like UDP-l-rhamnose and N1-acetylspermidine that have not been reported to be linked with CVD directly. Further, we also found that some metabolites like ethanolamide, solanidine, dimethylarginine, N-acetyl-l-tyrosine, can act as a discriminator of CVD. Metabolites integrating pathway enrichment analysis showed enrichment of various important metabolic pathways like histidine metabolism, methyl histidine metabolism, carnitine synthesis, along with arginine and proline metabolism in CVD patients. Our study provides a great opportunity to understand the pathophysiological role and impact of the identified unique metabolites and can be extrapolated as specific CVD specific metabolites.

Download Full-text

Formaldehyde and De/Methylation in Age-Related Cognitive Impairment

Genes ◽

10.3390/genes12060913 ◽

2021 ◽

Vol 12 (6) ◽

pp. 913

Author(s):

Ting Li ◽

Yan Wei ◽

Meihua Qu ◽

Lixian Mou ◽

Junye Miao ◽

...

Keyword(s):

Amino Acids ◽

Cell Proliferation ◽

Cognitive Impairment ◽

Metabolic Pathways ◽

Memory Formation ◽

Epigenetic Alterations ◽

Diagnostic Biomarker ◽

Reactive Substance ◽

Age Related ◽

Novel Therapeutic

Formaldehyde (FA) is a highly reactive substance that is ubiquitous in the environment and is usually considered as a pollutant. In the human body, FA is a product of various metabolic pathways and participates in one-carbon cycle, which provides carbon for the synthesis and modification of bio-compounds, such as DNA, RNA, and amino acids. Endogenous FA plays a role in epigenetic regulation, especially in the methylation and demethylation of DNA, histones, and RNA. Recently, epigenetic alterations associated with FA dysmetabolism have been considered as one of the important features in age-related cognitive impairment (ARCI), suggesting the potential of using FA as a diagnostic biomarker of ARCI. Notably, FA plays multifaceted roles, and, at certain concentrations, it promotes cell proliferation, enhances memory formation, and elongates life span, effects that could also be involved in the aetiology of ARCI. Further investigation of and the regulation of the epigenetics landscape may provide new insights about the aetiology of ARCI and provide novel therapeutic targets.

Download Full-text